nrcam scientific advisory board 1/25/2010 9:15coffee, donutsall 9:30introduction and overviewloew...
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NRCAM Scientific Advisory Board1/25/2010
9:15 Coffee, donuts All9:30 Introduction and Overview Loew9:45 Demo of New Virtual Cell Features Loew, Moraru, Schaff ,
Cowan11:00 TR&D Progress and Plans
1.Biophysical Mechanisms Carson, Rodionov, Brown
11:30 2. Numerical Tools Slepchenko
11:45 3. Enabling Technologies Schaff
12:00 4. Application Development Moraru
12:15 Lunch
12:45 Dissemination, Training Cowan, Holmes
1:00 Collaborations Loew, Slepchenko, Ruebenacker
1:30 Breakout SessionsBiology (Jacobson, Lederer, Pollard) E5036Math/Physics/Comp (Greengard, MacLeod, Tyson, Colella(remote)) L5095
Carson, Cowan, Loew, Rodionov, Holmes, et al.Slepchenko, Schaff, Moraru, Resasco, et al.
3:00 Advisors Executive Session L5095Report writing
Advisors
4:45 Read back of report, open discussion L5095 All5:30 Dinner L5095
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The TeamLes Loew – Co-PI; Biophysical MechanismsBoris Slepchenko – Co-PI, Numerical Tools and Algorithms Jim Schaff – Co-PI, Software Development Leader Ion Moraru – Co-PI, System Administrator/ArchitectAnn Cowan – Co-PI, Dissemination, Service, Training *Michael Blinov – Rule-based modeling *Sofya Borinskaya – Graduate Student * Sherry-Ann Brown – Graduate StudentJohn Carson – Co-I, Biophysical Mechanisms Yung-Sze Choi – Co-I, Mathematics *Jonathon Ditlev – Graduate Student *Jeff Dutton – System Manager and Support Fei Gao – Software Developer *Raquell Homes – Training, Dissemination *Pavel Kraykivskiy – Discrete models of cytoskeleton Susan Krueger – Website Developer, User facility *Anu Lakshminarayana – Software Developer Debbie Manchak - Administrative support ( funded through Institutional support) Frank Morgan – Software Developer *Igor Novak – Force-dependent integrin clustering, lateral diffusion, actin dynamicsDiana Resasco – Numerics Vladimir Rodionov – Co-I, Biophysical Mechanisms *Oliver Ruebenacker – Software developerIrina Semenova – Organelle Trafficking *Dan Vasilescu - Software developer*Charles Wolgemuth – Moving boundaries *Li Ye – Software Developer Karen Zucker – Program Coordinator (funded through Institutional support) --------------------------------(*supported via collaborative grants)
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Virtual Cell Capabilities
• Reaction - Diffusion - Advection - Electrophysiology• 0, 1, 2 or 3 D including geometries from microscope images• Stochastic simulators and Parameter Estimation for 0D• Database of models and model components• Biological Problems
– Signaling and metabolic pathways– Intracellular trafficking– Ion channels– Fluorescent indicators and probe redistribution
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The Big TR&D PictureThe Big TR&D Picture
Cell BiologyCell Biology
BiophysicalMechanisms
NumericalTools
EnablingTechnologies
ApplicationDevelopment
DeveloperDeveloperCommunityCommunity
PrototypeCode
MathModelWorkspace
BioModelWorkspace
StandaloneApplication
Drivers:Drivers:
WorkWorkflow:flow:
Products:Products:
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Biophysical MechanismsBiophysical Mechanisms1. Macromolecular Aggregation - FCS studies of RNA
delivery and translation in dendritic spines
2. Cytoskeletal dynamics – discrete spatial model of microtubule dynamics
3. Spatial electrophysiology – Computational methods for combined electrophysiological and biochemical modeling of neurons
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Numerical ToolsNumerical Tools
1. Implementation of stiff PDE solvers in VCell – New fully implicit solver has been tested and deployed.
2. Implementation of elliptic solvers – Using VCell Poisson solver in the study
of diffusion in crowded spaces
3. Adaptive meshes and parallelization – Major effort on adapting CHOMBO as a new solver for VCell
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Enabling TechnologiesEnabling Technologies
1. Prototype implementation of moving boundaries
2. Progress in plugin architecture permits application of Smoldyn spatial stochastic simulator to VCell BioModel
3. Relaxed topology constraints for cell-cell communication and electrophysiology modeling.
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Application DevelopmentApplication Development1. New software process – No news after last
year’s full conversion to Eclipse
2. New server components – Full deployment of OSG cluster; standalone solvers
3. New user-level functionality – The Biomodel GUI has been expanded with much more flexible methods for model formulation and simulation specification
4. New VCell applications and deployment – Separate VFRAP application is the first rollout of specialized apps.
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ImpactImpactFeb ‘09 – Jan ‘10
Feb-09
Total Registered VCell Users – 12,364Users Who Ran Simulations – 2,224Currently Stored Models – 29,117Currently Stored Simulations – 160,539Publicly Available Models – 687Publicly Available Simulations - 2,377
Jan-10
→ 13,249→ 2,526→ 34,402→ 183,339→ 720 → 2,778
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NewsNews
• New Deployed VCell Features (Demos)– Fully-Implicit Finite Volume Solver– Expressions for Advection and Diffusion in Biomodel– Geometries: segmentation support; analytical primitives– Generalized metadata and annotation support– GUI Improvements (auto complete; math description search and syntax highlight;
SPPR; global functions for sims; detailed solver descriptions…)– VFRAP
• TCNP Grant will end this summer – no-cost extension for 1 additional year
• Systems Biology Grant Submitted• SIG Grant for new cluster to be funded• CSHL CCB Symposium 3/24-27/09; in Hinxton 2/10-14/10• CSHL CCB course 6/25 – 7/16, 2009; again this coming summer, 7/2-
22/10
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NIGMS Systems Biology GrantPhysics of Cellular Systems
• A computational framework for spatial stochastic modeling of crowded molecular environments
• A computational framework for coarse grain modeling of molecular complexes• A computational framework for modeling sub-cellular stresses and strains• A computational infrastructure for integrating multiple physical formulations of
biological systems• A data-driven model of dendritic spine morphogenesis• A data-driven model of cell adhesion morphology and cytoskeletal interactions• A data-driven model of actin comet tail-driven propulsion• A data-driven model of cell migration in the developing C. elegans embryo• A UCONN Ph.D. training program in Cell Analysis and Modeling • Educational programs especially inclusive of traditionally underrepresented
populations• Adoption of new physics-based analysis by the systems biology and cell
biology research communities
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Cell And Genome Sciences Building
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Cell And Genome Sciences Building
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